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spacer_count is a optimized counter for spacers or barcodes from various type of sequencing outputs. It uses regex and pairwise alignment for sapcer detection, therefore it reliably count spacers appearing in any position and orientation of the read, and tolerate certain level of error (substitution and in-del). Thus, it can be used directly on outputs from sources like whole-plasmid sequencing (long-reads), staggered amplicon, or simply reads without adaptor trimming.
Performance optimization:
- Multiprocessing if enabled for pairwise alignment.
- LRU caching is enabled to accelerate error correction
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